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Potassium in PDB 6d7j: The Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) with Glycerol in Active-Site

Protein crystallography data

The structure of The Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) with Glycerol in Active-Site, PDB code: 6d7j was solved by M.S.Little, M.R.Redinbo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.34 / 2.24
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 92.920, 171.968, 125.322, 90.00, 107.84, 90.00
R / Rfree (%) 16.5 / 20

Other elements in 6d7j:

The structure of The Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) with Glycerol in Active-Site also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the The Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) with Glycerol in Active-Site (pdb code 6d7j). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the The Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) with Glycerol in Active-Site, PDB code: 6d7j:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in 6d7j

Go back to Potassium Binding Sites List in 6d7j
Potassium binding site 1 out of 4 in the The Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) with Glycerol in Active-Site


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of The Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) with Glycerol in Active-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K901

b:20.5
occ:1.00
 O A:VAL84 2.7 22.1 1.0
O A:ASP81 2.8 19.6 1.0
O A:ASP78 2.8 19.5 1.0
O A:ALA79 2.9 22.1 1.0
O A:HOH1211 3.0 13.9 1.0
CD2 A:TYR608 3.3 18.4 1.0
CE2 A:TYR608 3.3 19.8 1.0
C A:ALA79 3.5 19.6 1.0
CG A:TYR608 3.6 22.0 1.0
CZ A:TYR608 3.6 20.1 1.0
C A:ASP81 3.9 18.5 1.0
CD1 A:TYR608 3.9 17.2 1.0
C A:VAL84 3.9 20.7 1.0
O A:HOH1173 3.9 16.6 1.0
CE1 A:TYR608 3.9 17.9 1.0
C A:ASP78 4.0 19.3 1.0
N A:ASP81 4.1 20.5 1.0
N A:VAL80 4.2 17.7 1.0
CA A:ALA79 4.2 19.3 1.0
N A:TYR86 4.2 16.6 1.0
C A:VAL80 4.3 21.0 1.0
OH A:TYR608 4.4 21.9 1.0
CA A:VAL80 4.4 19.3 1.0
CB A:TYR608 4.4 18.6 1.0
CG2 A:VAL84 4.4 16.9 1.0
CA A:ASP81 4.4 19.7 1.0
N A:ALA79 4.6 21.5 1.0
C A:ASN85 4.6 19.8 1.0
N A:VAL84 4.7 24.3 1.0
CB A:TYR86 4.7 18.3 1.0
CB A:ASP81 4.7 19.2 1.0
CA A:ASN85 4.7 20.2 1.0
CA A:TYR86 4.8 16.9 1.0
N A:ASN85 4.8 21.1 1.0
CA A:VAL84 4.9 20.5 1.0
O A:VAL80 4.9 18.5 1.0
N A:PRO82 4.9 20.7 1.0

Potassium binding site 2 out of 4 in 6d7j

Go back to Potassium Binding Sites List in 6d7j
Potassium binding site 2 out of 4 in the The Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) with Glycerol in Active-Site


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of The Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) with Glycerol in Active-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K901

b:17.2
occ:1.00
 O B:VAL84 2.6 19.1 1.0
O B:ASP78 2.7 18.8 1.0
O B:HOH1195 2.8 14.2 1.0
O B:ASP81 2.8 18.7 1.0
O B:ALA79 2.9 18.7 1.0
C B:ALA79 3.4 16.6 1.0
CD2 B:TYR608 3.4 16.0 1.0
CE2 B:TYR608 3.5 16.4 1.0
CG B:TYR608 3.7 19.1 1.0
CZ B:TYR608 3.8 19.5 1.0
O B:HOH1095 3.8 13.1 1.0
C B:VAL84 3.9 18.1 1.0
C B:ASP78 3.9 17.0 1.0
C B:ASP81 3.9 17.6 1.0
CD1 B:TYR608 3.9 14.8 1.0
CE1 B:TYR608 4.0 20.8 1.0
N B:ASP81 4.1 18.3 1.0
CA B:ALA79 4.1 16.0 1.0
N B:TYR86 4.1 17.3 1.0
N B:VAL80 4.1 16.4 1.0
C B:VAL80 4.3 17.6 1.0
CA B:VAL80 4.4 19.1 1.0
CA B:ASP81 4.4 17.3 1.0
CB B:TYR608 4.5 18.5 1.0
N B:ALA79 4.5 15.5 1.0
OH B:TYR608 4.5 19.0 1.0
CG2 B:VAL84 4.5 17.2 1.0
C B:ASN85 4.6 16.7 1.0
CB B:TYR86 4.6 15.0 1.0
CA B:TYR86 4.7 17.6 1.0
CB B:ASP81 4.7 16.1 1.0
CA B:ASN85 4.7 15.2 1.0
N B:VAL84 4.7 21.2 1.0
N B:ASN85 4.7 19.1 1.0
CA B:VAL84 4.8 19.7 1.0
O B:VAL80 4.9 16.9 1.0

Potassium binding site 3 out of 4 in 6d7j

Go back to Potassium Binding Sites List in 6d7j
Potassium binding site 3 out of 4 in the The Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) with Glycerol in Active-Site


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of The Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) with Glycerol in Active-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K901

b:26.0
occ:1.00
 O C:VAL84 2.6 20.9 1.0
O C:ASP78 2.8 19.6 1.0
O C:ASP81 2.8 24.7 1.0
O C:ALA79 2.9 23.6 1.0
O C:HOH1234 2.9 18.5 1.0
CD1 C:TYR608 3.3 24.3 1.0
CE1 C:TYR608 3.3 22.8 1.0
C C:ALA79 3.5 23.2 1.0
CG C:TYR608 3.6 21.2 1.0
CZ C:TYR608 3.7 22.7 1.0
C C:VAL84 3.8 22.9 1.0
C C:ASP81 3.9 25.8 1.0
C C:ASP78 4.0 20.0 1.0
O C:HOH1171 4.0 19.2 1.0
CD2 C:TYR608 4.0 19.0 1.0
N C:ASP81 4.0 22.0 1.0
CE2 C:TYR608 4.0 18.0 1.0
N C:VAL80 4.1 22.1 1.0
N C:TYR86 4.1 24.9 1.0
CA C:ALA79 4.2 20.3 1.0
C C:VAL80 4.2 23.7 1.0
CA C:VAL80 4.3 25.3 1.0
CB C:TYR608 4.4 19.3 1.0
CA C:ASP81 4.4 24.8 1.0
CG2 C:VAL84 4.4 21.2 1.0
OH C:TYR608 4.5 19.2 1.0
N C:VAL84 4.6 25.1 1.0
C C:ASN85 4.6 25.5 1.0
N C:ALA79 4.6 19.5 1.0
CB C:ASP81 4.6 26.7 1.0
CB C:TYR86 4.7 19.5 1.0
CA C:ASN85 4.7 23.4 1.0
CA C:TYR86 4.7 22.0 1.0
N C:ASN85 4.7 21.5 1.0
CA C:VAL84 4.7 27.1 1.0
O C:VAL80 4.8 26.2 1.0
N C:PRO82 5.0 26.7 1.0

Potassium binding site 4 out of 4 in 6d7j

Go back to Potassium Binding Sites List in 6d7j
Potassium binding site 4 out of 4 in the The Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) with Glycerol in Active-Site


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of The Crystal Structure of Parabacteroides Merdae Beta-Glucuronidase (Gus) with Glycerol in Active-Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K901

b:24.3
occ:1.00
 O D:VAL84 2.6 24.2 1.0
O D:ASP81 2.7 27.2 1.0
O D:ASP78 2.8 26.6 1.0
O D:ALA79 2.8 26.6 1.0
O D:HOH1254 2.9 23.4 1.0
CE2 D:TYR608 3.3 22.9 1.0
CD2 D:TYR608 3.3 25.4 1.0
C D:ALA79 3.5 26.0 1.0
CZ D:TYR608 3.7 25.4 1.0
CG D:TYR608 3.7 26.1 1.0
C D:ASP81 3.8 29.6 1.0
C D:VAL84 3.8 25.2 1.0
C D:ASP78 4.0 27.8 1.0
CD1 D:TYR608 4.0 23.0 1.0
CE1 D:TYR608 4.0 21.7 1.0
O D:HOH1138 4.0 20.5 0.7
N D:ASP81 4.0 25.9 1.0
N D:TYR86 4.1 21.9 1.0
N D:VAL80 4.2 23.7 1.0
CA D:ALA79 4.2 26.1 1.0
C D:VAL80 4.2 31.3 1.0
CA D:ASP81 4.4 28.4 1.0
OH D:TYR608 4.4 22.5 1.0
CA D:VAL80 4.4 23.0 1.0
CG2 D:VAL84 4.4 22.3 1.0
CB D:TYR608 4.5 22.6 1.0
C D:ASN85 4.6 25.9 1.0
CB D:ASP81 4.6 29.6 1.0
N D:ALA79 4.6 24.0 1.0
N D:VAL84 4.6 26.8 1.0
CB D:TYR86 4.7 22.9 1.0
CA D:TYR86 4.7 25.8 1.0
CA D:ASN85 4.7 27.8 1.0
N D:ASN85 4.7 27.5 1.0
CA D:VAL84 4.8 25.1 1.0
O D:VAL80 4.9 29.9 1.0
N D:PRO82 4.9 29.5 1.0

Reference:

M.S.Little, M.R.Redinbo. Structural Basis For Parabacteroides Merdae Beta-Glucuronidase (Gus) Glycosaminoglycan Metabolism and Recognition of Alginate To Be Published.
Page generated: Mon Aug 12 15:43:36 2024

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